The G-patch protein Spp2 couples the spliceosome-stimulated ATPase activity of the DEAH-box protein Prp2 to catalytic activation of the spliceosome

Abstract

Structural rearrangement of the activated spliceosome (B act ) to yield a catalytically active complex (B*) is mediated by the DEAH-box NTPase Prp2 in cooperation with the G-patch protein Spp2. However, how the energy of ATP hydrolysis by Prp2 is coupled to mechanical work and what role Spp2 plays in this process are unclear. Using a purified splicing system, we demonstrate that Spp2 is not required to recruit Prp2 to its bona fide binding site in the B act spliceosome. In the absence of Spp2, the B act spliceosome efficiently triggers Prp2's NTPase activity, but NTP hydrolysis is not coupled to ribonucleoprotein (RNP) rearrangements leading to catalytic activation of the spliceosome. Transformation of the B act to the B* spliceosome occurs only when Spp2 is present and is accompanied by dissociation of Prp2 and a reduction in its NTPase activity. In the absence of spliceosomes, Spp2 enhances Prp2's RNA-dependent ATPase activity without affecting its RNA affinity. Our data suggest that Spp2 plays a major role in coupling Prp2's ATPase activity to remodeling of the spliceosome into a catalytically active machine.[Keywords: spliceosome activation; DEAH-box helicase; Prp2; G-patch protein; Spp2; ATP hydrolysis] Supplemental material is available for this article. Pre-mRNA splicing proceeds by way of two phosphoester transfer reactions and is catalyzed by the spliceosome, which consists of the U1, U2, U4/U6, and U5 small nuclear ribonucleoproteins (snRNPs) and numerous nonsnRNP proteins (Wahl et al. 2009). Spliceosome assembly occurs de novo on each pre-mRNA and follows an intricate pathway involving major structural rearrangements during each round of splicing. The various remodeling steps are driven in yeast by eight conserved DExD/H-box ATPases/ RNA helicases. An interesting feature of the spliceosome is that it initially assembles into a multimegadalton ensemble-termed complex B-that contains all of the snRNPs but does not yet have an active site. Activation of the spliceosome is then initiated by the combined action of the Prp28 and Brr2 RNA helicases, yielding the B act complex. In this process, U1 and U4 snRNPs are displaced from the spliceosome, and new base-pair interactions between the U6 and U2 snRNAs and between U6 and the 59 splice site (59SS) are formed. The resulting RNA structure plays a central role in catalyzing both steps of pre-mRNA splicing (Staley and Guthrie 1998;Fica et al. 2013). During activation, 20 new proteins, including those of the NTC (nineteen complex), are stably integrated into the B act complex and stabilize the newly formed RNA-RNA interaction network (Chan et al. 2003;Chan and Cheng 2005;Fabrizio et al. 2009). The final catalytic activation of the spliceosome requires an additional ATP-dependent remodeling step, yielding complex B*. This step is catalyzed by the DEAH-box ATPase Prp2 (Kim and Lin 1996).Prp2 is structurally related to three other spliceosomal DEAH-box ATPases: Prp16, Prp22, and Prp43, which are involved, respectively, in the second catalytic step, the

Limited Portability of G-Patch Domains in Regulators of the Prp43 RNA Helicase Required for Pre-mRNA Splicing and Ribosomal RNA Maturation in Saccharomyces cerevisiae

“…Lysine residues within this domain can be chemically cross-linked with the Spp382 G-patch consistent with close and perhaps direct contact between these peptide features (Christian et al 2014). Similar interactions are predicted to occur between the C-terminus of the Prp2 DEAHbox helicase and its G-patch activator, Spp2 (Roy et al 1995;Silverman et al 2004;Warkocki et al 2015). It was surprising, therefore, that the large Prp43 C-terminal domain (CTD) deletion scored here had no discernible impact on G-patch-dependent Spp382-Prp43 Y2H interaction.…”

Spliceosomal DEAH-Box ATPases Remodel Pre-mRNA to Activate Alternative Splice Sites

“…First, the SF2 ATPase Brr2 disrupts base-pairing between U6 and U4 snRNA to permit formation of interactions within U6 and between U6 and U2 snRNA, giving rise to the pre-catalytic spliceosome (Wahl et al, 2009). Then, the SF2 ATPase Prp2 promotes a more subtle rearrangement required for branching (Krishnan et al, 2013; Ohrt et al, 2012; Warkocki et al, 2015; Wlodaver and Staley, 2014). Following branching, the SF2 ATPase Prp16 and the Slu7/Prp18 heterodimer act sequentially to reposition the substrate and enable 3’ splice site recognition for exon ligation (James et al, 2002; Ohrt et al, 2013).…”

Role of Cwc24 in the First Catalytic Step of Splicing and Fidelity of 5′ Splice Site Selection

“…After the spliceosome has been activated, Prp2 mediates destabilization of the U2 snRNP com-ponents SF3a and SF3b, presumably to expose the branch point to allow the transesterification reaction (15)(16)(17)(18)(19), and the NTC-related proteins Cwc24 and Cwc27 are concomitantly removed from the spliceosome (15,16). The G-patch protein Spp2 is required for spliceosome association and functioning of Prp2 (14,(20)(21)(22). Another NTC-related protein, Cwc22, has also been shown to be necessary for the Prp2 functioning step (23).…”